The American Academy of Microbiology convened a colloquium November 6-7, 2003, in Key Largo, Florida, to discuss the application of genomic methods to the study of pathogenesis. Professionals in the fields of genomics, bacteriology, virology, eukaryotic microbiology, medicine, clinical diagnostics, bioinformatics, and forensics contributed their expertise to discussions on the recent advancements in the field and the outlook for future research. A number of recommendations were made for ensuring that progress in the field continues.

The availability of genome sequences from pathogenic bacteria, viruses, and fungi and other eukaryotes has opened new horizons for the field of pathogenesis. The genomes of over 100 bacterial pathogens have been fully sequenced, and scientists are busy investigating the mechanisms that regulate the diversity of bacterial pathogens and their myriad abilities to evade host defenses. Close to 1,200 viral genomes have been sequenced, and virologists are now beginning to examine the genomes of those viruses that cause undetected, cryptic infections. These virus-host interactions can serve as a reservoir of viral genes that later emerge in novel pathogens with the potential to infect humans, economically important animals, or crops. A number of eukaryotic microbes, including several pathogenic fungi, have also been sequenced, revealing unimagined diversity among these important pathogens.

Certain themes have emerged from analyses of pathogen genome sequences, and the possibility exists that a sequence-based “common thread” may be found linking pathogens from different taxa. The results of genome sequencing efforts have also informed the study of pathogenesis, helping to identify the ways in which pathogens bring about disease.

The advances of the past several years have been great, and we are closer than ever to a comprehensive understanding of pathogenesis, but much work lies ahead. If the science is to move forward, the genome sequences of many more organisms are needed. The sequences of many hosts, pathogens, their nonpathogenic relatives, commensals, as well as a diverse array of microorganisms, are all needed to complete the picture of pathogenesis and provide a phylogenetic framework for understanding the phenomenon. Moreover, improvements are needed in the two most important tools of genomics: annotation methodologies and sequence databases.